Flattening (FHIR to CSV)

Transforms FHIR NDJSON into CSV files using SQL-on-FHIR ViewDefinitions.

Requirements

• Pipeline must start with a CRTDL file
• fhir-flattener service running
• Lookup table configured

Configuration

services:
  flattening:
    service_url: "http://fhir-flattener:8000"
    lookup_path: "/path/to/flatten-lookup.json"
    formats:
      - csv
    timeout: 30m

pipeline:
  enabled_steps:
    - local_import
    - dimp
    - flattening

Configuration Options

Option	Type	Default	Description
service_url	string	-	fhir-flattener service URL
lookup_path	string	-	Path to lookup table file
formats	[]string	["csv"]	Output formats
timeout	duration	30m	Request timeout

How it Works

1. Parses CRTDL file to extract attribute groups
2. Builds ViewDefinitions from lookup tables
3. Filters resources by profile
4. Sends data to fhir-flattener service
5. Writes CSV files for each attribute group

Output

CSV files are written to jobs/<job-id>/csv/, one file per attribute group.